Download - Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation
Single-chromosome transcriptional profiling reveals chromosomal
gene expression regulation
Marshall J Levesque, Arjun RajSystems Biology LabUPenn Bioengineering
Nature Methods (2013) doi:10.1038/nmeth.2372
Thursday, April 11, 13
Our genome is organized into pairs of chromosomes
By 718 Bot at en.wikipedia [Public domain], from Wikimedia Commons. http://en.wikipedia.org/wiki/Karyotype
Thursday, April 11, 13
Chromosome rearrangements are a hallmark of cancer
Macville et al. Comprehensive and definitive molecular cytogenetic characterization of HeLa cells by spectral karyotyping. Cancer Res (1999) vol. 59 (1) pp. 141-50
Thursday, April 11, 13
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Does chromosome structure affect gene expression?
RNA FISH (fluorescence in situ hybridization) from Raj Lab website image gallery
Thursday, April 11, 13
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
RNA FISH (fluorescence in situ hybridization) from Raj Lab website image gallery
Does chromosome structure affect gene expression?
Thursday, April 11, 13
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Does chromosome structure affect gene expression?
RNA FISH (fluorescence in situ hybridization) from Raj Lab website image gallery
Thursday, April 11, 13
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
RNA counting cannot tell us where the RNA comes from
RNA FISH (fluorescence in situ hybridization) from Raj Lab website image gallery
Thursday, April 11, 13
iceFISH assay detects active genes on single chromosomes
Spliced mRNA
Export andTranslation
ExonExon
Exon
IntronIntron
Introns degraded beforeleaving site of transcription
mRNA
Raj et al. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods (2008)
Thursday, April 11, 13
iceFISH assay detects active genes on single chromosomes
Spliced mRNA
Export andTranslation
ExonExon
Exon
IntronIntron
Introns degraded beforeleaving site of transcription
intron
Thursday, April 11, 13
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
Pseudocoloring provides 20+ unique tags to trace a chromosome
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
Thursday, April 11, 13
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
Pseudocoloring provides 20+ unique tags to trace a chromosome
Thursday, April 11, 13
iceFISH assigns gene activity to normal or derivative copies of chr19
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Thursday, April 11, 13
Translocations can lead to whole chromosome increases in expression
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)RP
L18A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Thursday, April 11, 13
Translocations do not necessarily lead to changes in transcriptional activity
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
to Chr 6 centromere
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
iceF
ISH
spo
ts p
er c
hrom
osom
e
Thursday, April 11, 13
Are chromosomes built to regulate their genes?
Chr. 19EEF2 mRNAEEF2 intron
Thursday, April 11, 13
Single chromosome transcription profiles unravel gene interactions
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PSRPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
Anti-Correlated Expression
Correlated Expression
Uncorrelated Expression
Thursday, April 11, 13
Measured gene activity shows interactions at chromosome scale
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
-log(p)
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
RPS19PTBP1EEF2DNMT1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEG
LN2RPS19
OFF
OFF
ZNF444
ON
ON
RPS19OFF
OFF
ZNF444
ON
ON
RPS19OFF
OFF
ZNF444
ON
ON
RPS19OFF
OFF
ZNF444
ON
ON
Nucleus
Chr. 19G
ene A
Gene B
p = 2.7x10 -5
R = -0.42p = 1.0R = 0.008
p = 4.0x10 -5
R = -0.40p = 6.9x10 -4
R = 0.33TO
MM
40M
ARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNM
T1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEG
LN2RPS19TO
MM
40M
ARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNM
T1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEG
LN2RPS19TO
MM
40M
ARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNM
T1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEG
LN2RPS19TO
MM
40M
ARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNM
T1ILF3DHPS
Intra-chromosom
al (cis) interactionsInter-chrom
osomal (trans) interactions
4531527
2749239
4524625
35341615
Nucleus
Chr. 19G
ene A
Gene B
1 2 p=0.05
4 p = 0.015 6 p = 0.001
8 p = 0.0001
High likelihood
of interaction
Low likelihood
of interaction
Human foreskin fibroblastsHeLa cells
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
Thursday, April 11, 13
Measured gene activity shows interactions at chromosome scale
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
-log(p)
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
RPS19PTBP1EEF2DNMT1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEG
LN2RPS19
OFF
OFF
ZNF444
ON
ON
RPS19OFF
OFF
ZNF444
ON
ON
RPS19OFF
OFF
ZNF444
ON
ON
RPS19OFF
OFF
ZNF444
ON
ON
Nucleus
Chr. 19G
ene A
Gene B
p = 2.7x10 -5
R = -0.42p = 1.0R = 0.008
p = 4.0x10 -5
R = -0.40p = 6.9x10 -4
R = 0.33TO
MM
40M
ARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNM
T1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEG
LN2RPS19TO
MM
40M
ARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNM
T1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEG
LN2RPS19TO
MM
40M
ARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNM
T1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEG
LN2RPS19TO
MM
40M
ARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNM
T1ILF3DHPS
Intra-chromosom
al (cis) interactionsInter-chrom
osomal (trans) interactions
4531527
2749239
4524625
35341615
Nucleus
Chr. 19G
ene A
Gene B
1 2 p=0.05
4 p = 0.015 6 p = 0.001
8 p = 0.0001
High likelihood
of interaction
Low likelihood
of interaction
Human foreskin fibroblastsHeLa cells -log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
Thursday, April 11, 13
Measured gene activity shows interactions at chromosome scale
Anti-Correlated
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
14Mb
Thursday, April 11, 13
Long range cis interaction is maintained in HeLa cell line
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
normal chromosome 19
Thursday, April 11, 13
Long range cis interaction is lost in rearranged chromosome 19
-log(p)
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
t(13;19)Gene A
Gene B
p = 1.0R = 0.03
p = 0.14R = 0.29
Intra-chromosomal (cis) interactions
HeLa cells, t(13;19)
Biol
ogica
l rep
licat
e 1
Com
bine
d da
tase
tBi
olog
ical r
eplic
ate
2
23
196
74
63
1
2
p = 0.05
4
p = 0.01
5
6
p = 0.001RP
L18A
UBA5
2ZN
F91
UBA2
EIF3
KSU
PT5H
FBL
EGLN
2RP
S19
TOM
M40
MAR
K4SL
C1A5
PPP2
R1A
RPS9
ZNF4
44
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
RPS1
9
OFF
OFFZNF444
ON
ON
p = 0.33R = 0.33
97
259
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
Supplementary Figure ***
Supplementary Fig. ***. Characterization of intra-chromosomal interactions between chromosome 19 gene pairs on the der(19)t(13;19) fusion chromosome in HeLa cells. The analysis is exactly the same as that performed in Fig. 3 and as described in the methods. We found no significant correlation between RPS19 and ZNF444, suggesting that the translocation disrupts the whatever the regulatory mechanism is that is respon-sible for the anti-correlation we obseved between this pair of genes on the normal copies of chromosome 19 in both human foreskin fibroblasts and HeLa cells.
High likelihoodof interaction
Low likelihoodof interaction
HeLa t(13;19)-log(p)
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPS1
9PT
BP1
EEF2
DNM
T1IL
F3DH
PS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
Chr. 19Gene A
Gene B
p = 2.7x10-5
R = -0.42p = 1.0R = 0.008
p = 4.0x10-5
R = -0.40p = 6.9x10-4
R = 0.33TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
PTBP
1EE
F2DN
MT1
ILF3
DHPS
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
PTBP1EEF2DNMT1ILF3DHPS
Intra-chromosomal (cis) interactions Inter-chromosomal (trans) interactions
4531
527
2749
239
4524
625
3534
1615
Nucleus
Chr. 19Gene A
Gene B
1
2
p=0.05
4
p = 0.015
6
p = 0.001
8
p = 0.0001
High likelihoodof interaction
Low likelihoodof interaction
Hum
an fo
resk
in fi
brob
last
sHe
La c
ells
-log(p)
RPS1
9
OFF
OFFZNF444
ON
ON
RPS1
9
OFF
OFFZNF444
ON
ON
Nucleus
t(13;19)Gene A
Gene B
p = 1.0R = 0.03
p = 0.14R = 0.29
Intra-chromosomal (cis) interactions
HeLa cells, t(13;19)
Biol
ogica
l rep
licat
e 1
Com
bine
d da
tase
tBi
olog
ical r
eplic
ate
2
23
196
74
63
1
2
p = 0.05
4
p = 0.01
5
6
p = 0.001
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
RPS1
9
OFF
OFFZNF444
ON
ON
p = 0.33R = 0.33
97
259
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
RPL1
8AUB
A52
ZNF9
1UB
A2EI
F3K
SUPT
5HFB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5PP
P2R1
ARP
S9ZN
F444
RPL18AUBA52ZNF91UBA2EIF3KSUPT5HFBLEGLN2RPS19TOMM40MARK4SLC1A5PPP2R1ARPS9ZNF444
Supplementary Figure ***
Supplementary Fig. ***. Characterization of intra-chromosomal interactions between chromosome 19 gene pairs on the der(19)t(13;19) fusion chromosome in HeLa cells. The analysis is exactly the same as that performed in Fig. 3 and as described in the methods. We found no significant correlation between RPS19 and ZNF444, suggesting that the translocation disrupts the whatever the regulatory mechanism is that is respon-sible for the anti-correlation we obseved between this pair of genes on the normal copies of chromosome 19 in both human foreskin fibroblasts and HeLa cells.
High likelihoodof interaction
Low likelihoodof interaction
Thursday, April 11, 13
Anti-Correlated
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
14Mb
Long range cis interaction is lost in rearranged chromosome 19
Thursday, April 11, 13
Anti-Correlated
14Mb0
48
1216
20
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
Long range cis interaction is lost in rearranged chromosome 19
Thursday, April 11, 13
Anti-Correlated
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
14Mb
04
812
1620
1612
84
0
024
x (µm)
y (µm)
z (µ
m)
C DAPI ED ATTO488 Cy3
F G HAlexa 594 ATTO647N ATTO700
Chromosome 19IntronA
5 base colors
2 colors 3 colors20 pseudocolors
B
I
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
JChr 19
Chr 19
Nucleus
iceFISH revealed new chromosome-level gene expression behaviors
Chr 19
Chr 19t(13;19)
Fusionchromosomes
t(6;19)
DIAPH3MTZ1 RPL18A UBA52 ZNF91 UBA2 EIF3K SUPT5H FBL EGLN2 RPS19 TOMM40 MARK4 SLC1A5 PPP2R1A RPS9 ZNF444
HeLa Karyotype
Chr 19
Chr 19q-arm
*** **
** ***
******
******
***
***
Chr 6p-arm
Chr 6q-arm
Chr 19p-arm
Chromosome 19 gene name
Chromosome 19 gene name
Chr. 13gene name
0
0.4
0.2
0.8
1
0.6
iceFI
SH s
pots
per
chr
omos
ome
t(13;19)
t(6;19)Chr 13q-arm
A
C
B
CentromereTranslocation
t(13;19) t(13;19)
Chr 19Chr 13t(13;19)t(6;19)
PTBP1 EEF2 DNMT1 ILF3 DHPS 0
0.4
0.2
0.8
1
0.6
t(6;19)
RPL1
8A
UBA5
2
ZNF9
1
UBA2
EIF3
KSU
PT5H FB
LEG
LN2
RPS1
9TO
MM
40M
ARK4
SLC1
A5
PPP2
R1A
RPS9
ZNF4
44
PTBP
1
EEF2
0 Mb Chromosome 19 59.13 Mb
DNM
T1IL
F3DH
PS
N=30N=50
N=30
Thursday, April 11, 13
Acknowledgements
Members of the Raj Lab
Morrissette Cytogenetics Lab
Biosearch Technologies
Thursday, April 11, 13